knitr::opts_chunk$set( collapse = TRUE, warning = TRUE, message = TRUE, width = 120, comment = "#>", fig.retina = 2, fig.path = "README-" )
This vignette demonstrates the easiest way to use autotest
, which is to apply
it continuously through the entire process of package development. The best way
to understand the process is to obtain a local copy of the vignette itself from
this
link,
and step through the code. We begin by constructing a simple package in the
local
tempdir()
.
To create a package in one simple line, we use
usethis::create_package()
,
and name our package "demo"
.
path <- file.path (tempdir (), "demo") usethis::create_package (path, check_name = FALSE, open = FALSE)
The structure looks like this:
fs::dir_tree (path)
Having constructed a minimal package structure, we can then insert some code in
the R/
directory, including initial roxygen2
documentation lines, and use the roxygenise()
function to create the
corresponding man
files.
autotest
works by parsing and running "example" code from function
documentation, so our code needs to include at least one example line.
code <- c ("#' my_function", "#'", "#' @param x An input", "#' @return Something else", "#' @examples", "#' y <- my_function (x = 1)", "#' @export", "my_function <- function (x) {", " return (x + 1)", "}") writeLines (code, file.path (path, "R", "myfn.R")) roxygen2::roxygenise (path)
Our package now looks like this:
fs::dir_tree (path)
We can already apply autotest
to that package to see what happens, first
ensuring that we've loaded the package ready to use.
library (autotest) x0 <- autotest_package (path)
devtools::load_all (".", export_all = FALSE) x0 <- autotest_package (path)
We use the DT
package to display the results
here.
DT::datatable (x0, options = list (dom = "t")) # display table only
The first thing to notice is the first column, which has test_type = "dummy"
for all rows. The autotest_package()
function
has a parameter test
with a default value of FALSE
, so that the default
call demonstrated above does not actually implement the tests, rather it
returns an object listing all tests that would be performed with actually doing
so. Applying the tests by setting test = TRUE
gives the following result.
x1 <- autotest_package (path, test = TRUE) DT::datatable (x1, options = list (dom = "t"))
Of the r nrow(x0)
tests which were performed, only r nrow(x1)
yielded
unexpected behaviour. The first indicates that the parameter x
has only been
used as an integer, yet was not specified as such. The second states that the
parameter x
is "assumed to be a single numeric". autotest
does its best to
figure out what types of inputs are expected for each parameter, and with the
example only demonstrating x = 1
, assumes that x
is always expected to be
a single value. We can resolve the first of these by replacing x = 1
with x
= 1.
to clearly indicate that it is not an integer, and the second by
asserting that length(x) == 1
, as follows:
code <- c ("#' my_function", "#'", "#' @param x An input", "#' @return Something else", "#' @examples", "#' y <- my_function (x = 1.)", "#' @export", "my_function <- function (x) {", " if (length(x) > 1) {", " warning(\"only the first value of x will be used\")", " x <- x [1]", " }", " return (x + 1)", "}") writeLines (code, file.path (path, "R", "myfn.R")) roxygen2::roxygenise (path)
This is then sufficient to pass all autotest
tests and so return NULL
.
autotest_package (path, test = TRUE)
Note that autotest
distinguishes integer and non-integer types by their
storage.mode
of "integer"
and "double"
, and not by their respective classes of
"integer"
and "numeric"
, because "numeric"
is ambiguous in R, and
is.numeric(1L)
is TRUE
, even though storage.mode(1L)
is "integer"
, and
not "numeric"
. Replacing x = 1
with x = 1.
explicitly identifies that
parameter as a "double"
parameter, and allowed the preceding tests to pass.
Note what happens if we instead specify that parameter as an integer (x =
1L
).
code [6] <- gsub ("1\\.", "1L", code [6]) writeLines (code, file.path (path, "R", "myfn.R")) roxygen2::roxygenise (path) x2 <- autotest_package (path, test = TRUE) DT::datatable (x2, options = list (dom = "t"))
That then generates two additional messages, the second of which reflects an
expectation that parameters assumed to be integer-valued should assert that,
for example by converting with as.integer()
. The following suffices to remove
that message.
code <- c (code [1:12], " if (is.numeric (x))", " x <- as.integer (x)", code [13:length (code)])
The remaining message concerns integer ranges. For any parameters which
autotest
identifies as single integers, routines will try a full range of
values between +/- .Machine$integer.max
, to ensure that all values are
appropriately handled. Many routines may sensibly allow unrestricted ranges,
while many others may not implement explicit control over permissible ranges,
yet may error on, for example, unexpectedly large positive or negative values.
The content of the diagnostic message indicates one way to resolve this issue,
which is simply by describing the input as "unrestricted"
.
code [3] <- gsub ("An input", "An unrestricted input", code [3]) writeLines (code, file.path (path, "R", "myfn.R")) roxygen2::roxygenise (path) autotest_package (path, test = TRUE)
An alternative, and frequently better way, is to ensure and document specific control over permissible ranges, as in the following revision of our function.
code <- c ("#' my_function", "#'", "#' @param x An input between 0 and 10", "#' @return Something else", "#' @examples", "#' y <- my_function (x = 1L)", "#' @export", "my_function <- function (x) {", " if (length(x) > 1) {", " warning(\"only the first value of x will be used\")", " x <- x [1]", " }", " if (is.numeric (x))", " x <- as.integer (x)", " if (x < 0 | x > 10) {", " stop (\"x must be between 0 and 10\")", " }", " return (x + 1L)", "}") writeLines (code, file.path (path, "R", "myfn.R")) roxygen2::roxygenise (path) autotest_package (path, test = TRUE)
Respective limits of ranges may be specified with any of the following words:
The initial test results above suggested that the input was assumed to be of length one. Let us now revert our function to its original format which accepted vectors of length > 1, and include an example demonstrating such input.
code <- c ("#' my_function", "#'", "#' @param x An input", "#' @return Something else", "#' @examples", "#' y <- my_function (x = 1)", "#' y <- my_function (x = 1:2)", "#' @export", "my_function <- function (x) {", " if (is.numeric (x)) {", " x <- as.integer (x)", " }", " return (x + 1L)", "}") writeLines (code, file.path (path, "R", "myfn.R")) roxygen2::roxygenise (path)
Note that the first example no longer has x = 1L
. This is because vector
inputs are identified as integer
by examining all individual values, and
presuming integer
representations for any parameters for which all values are
whole numbers, regardless of storage.mode
.
x3 <- autotest_package (path, test = TRUE) DT::datatable (x3, options = list (dom = "t"))
The above result reflects one of the standard tests, which is to determine
whether list-column formats are appropriately processed. List-columns commonly
arise when using (either directly or indirectly), the tidyr::nest()
function, or equivalently in
base R with the I
or AsIs
function.
They look like this:
dat <- data.frame (x = 1:3, y = 4:6) dat$x <- I (as.list (dat$x)) # base R dat <- tidyr::nest (dat, y = y) print (dat)
The use of packages like tidyr
and
purrr
quite often leads to
tibble
-class inputs which contain
list-columns. Any functions which fail to identify and appropriately respond to
such inputs may generate unexpected errors, and this autotest
is intended to
enforce appropriate handling of these kinds of inputs. The following lines
demonstrate the kinds of results that can arise without such checks.
m <- mtcars head (m, n = 2L) m$mpg <- I (as.list (m$mpg)) head (m, n = 2L) # looks exaxtly the same cor (m)
In contrast, many functions either assume inputs to be lists, and convert when
not, or implicitly unlist
. Either way, such functions may respond entirely
consistently regardless of the presence of list-columns, like this:
m$mpg <- paste0 ("a", m$mpg) class (m$mpg)
The list-column autotest
is intended to enforce consistent behaviour in
response to list-column inputs. One way to identify list-column formats is to
check the value of class(unclass(.))
of each column. The unclass
function
is necessary to first remove any additional class attributes, such as I
in
dat$x
above. A modified version of our function which identifies and responds
to list-column inputs might look like this:
code <- c ("#' my_function", "#'", "#' @param x An input", "#' @return Something else", "#' @examples", "#' y <- my_function (x = 1)", "#' y <- my_function (x = 1:2)", "#' @export", "my_function <- function (x) {", " if (methods::is (unclass (x), \"list\")) {", " x <- unlist (x)", " }", " if (is.numeric (x)) {", " x <- as.integer (x)", " }", " return (x + 1L)", "}") writeLines (code, file.path (path, "R", "myfn.R")) roxygen2::roxygenise (path)
That change once again leads to clean autotest
results:
autotest_package (path, test = TRUE)
Of course simply attempting to unlist
a complex list-column may be dangerous,
and it may be preferable to issue some kind of message or warning, or even
either simply remove any list-columns entirely or generate an error. Replacing
the above, potentially dangerous, line, x <- unlist (x)
with a simple
stop("list-columns are not allowed")
will also produce clean autotest
results.
Functions which return complicated results, such as objects with specific
classes, need to document those class types, and autotest
compares return
objects with documentation to ensure that this is done. The following code
constructs a new function to demonstrate some of the ways autotest
inspects
return objects, demonstrating a vector input (length(x) > 1
) in the example
to avoid messages regarding length checks an integer ranges.
code <- c ("#' my_function3", "#'", "#' @param x An input", "#' @examples", "#' y <- my_function3 (x = 1:2)", "#' @export", "my_function3 <- function (x) {", " return (datasets::iris)", "}") writeLines (code, file.path (path, "R", "myfn3.R")) roxygen2::roxygenise (path) # need to update docs with seed param x4 <- autotest_package (path, test = TRUE) DT::datatable (x4, options = list (dom = "t"))
Several new diagnostic messages are then issued regarding the description of the returned value. Let's insert a description to see the effect.
code <- c (code [1:3], "#' @return The iris data set as dataframe", code [4:length (code)]) writeLines (code, file.path (path, "R", "myfn3.R")) roxygen2::roxygenise (path) # need to update docs with seed param x5 <- autotest_package (path, test = TRUE) DT::datatable (x5, options = list (dom = "t"))
That result still contains a couple of diagnostic messages, but it is now
pretty clear what we need to do, which is to be precise with our specification
of the class of return object. The following then suffices to once again
generate clean autotest
results.
code [4] <- "#' @return The iris data set as data.frame" writeLines (code, file.path (path, "R", "myfn3.R")) roxygen2::roxygenise (path) # need to update docs with seed param autotest_package (path, test = TRUE)
Similar checks are performed on the documentation of input parameters, as demonstrated by the following modified version of the preceding function.
code <- c ("#' my_function3", "#'", "#' @param x An input", "#' @return The iris data set as data.frame", "#' @examples", "#' y <- my_function3 (x = datasets::iris)", "#' @export", "my_function3 <- function (x) {", " return (x)", "}") writeLines (code, file.path (path, "R", "myfn3.R")) roxygen2::roxygenise (path) # need to update docs with seed param x6 <- autotest_package (path, test = TRUE) DT::datatable (x6, options = list (dom = "t"))
This warning again indicates precisely how it can be rectified, for example by replacing the third line with
code [3] <- "#' @param x An input which can be a data.frame"
The demonstrations above hopefully suffice to indicate the general procedure
which autotest
attempts to make as simple as possible. This procedure
consists of the following single point:
autotest_package()
returns NULL
.This vignette has only demonstrated a few of the tests included in the package,
but as long as you use autotest
throughout the entire process of package
development, any additional diagnostic messages should include sufficient
information for you to be able to restructure your code to avoid them.
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